Soil aggregate stability is often used as the key indicate to evaluate soil degradation or soil erodibility. Numerous studies have indicated that biological soil crusts (biocrusts) can stabilise the soil surface by increasing the aggregate stability. In the end of the 20th century, the “Grain for Green” ecological project was implemented in most areas of the Loess Plateau, leading to the widespread distribution and succession of biocrusts in the open spaces between vascular plants in the abandoned farmlands. However, the effects of biocrust succession on the soil aggregate stability of subsurface remain poorly explored. Thus, to determine how biocrust succession affect subsurface soil aggregate stability, we investigated a cropland and 5 abandoned farmlands sites that have developed over three to 30 years in the Loess Plateau region of China. Then we measured the amounts of water stable aggregates of subsurface soil underlying different successional stage biocrusts (bare soil, cyanobacterial crust, cyanobacteria-moss mixed crust, and moss crust) by using wet-sieving method, and summed the mass fraction of soil remaining on each sieve after sieving multiplied by the mean aperture of the adjacent mesh (mean weight diameter) to characterise the soil aggregate stability. In addition, we analysed the complex correlations among age of farmland abandonment, biocrust succession, soil organic matter, clay fraction, and aggregate stability using structural equation modelling (SEM). The results are as follows: (1) the mean weight diameter (MWD) in the subsurface soil increased with the biocrust succession. The MWD in the 0–2-cm soil layer beneath moss crusts was 2.33 mm, 7.3 times as much as that of cropland sites. (2) The later successional stage biocrusts (mixed crust and moss crust) improved the deeper soil aggreggate stability compared with the early successional stage biocrusts. The MWD in 0–2-cm layer of the cyanobacterial crust was significantly higher than those of the lower layers, while MWDs in 0–2-cm and 0–5-cm layers of the later successional stage biocrust were significantly higher than that of 5–10-cm layer. (3) The SEM results confirmed that in the 0–5-cm layer, biocrust succession indirectly improved the stability of aggregates by increasing soil organic matter (SOM). There was a highly significant linear relationship between MWD of 0–5-cm layer and biocrust succession parameter (moss biomass) (R2 = 0.35, P = 0.002). In the 5–10-cm layer, the SOM still significantly influenced the aggregate stability, but the biocrusts had no significant effect on the SOM in this layer. The results suggest that biocrusts should be considered a crucial factor in soil stability and be used as an effective rehabilitative tool for restoring lands in dryland regions.